title: The emergence of top-down proteomics in clinical research.
abstract: Proteomic technology has advanced steadily since the development of 'soft-ionization' techniques for mass-spectrometry-based molecular identification more than two decades ago. Now, the large-scale analysis of proteins (proteomics) is a mainstay of biological research and clinical translation, with researchers seeking molecular diagnostics, as well as protein-based markers for personalized medicine. Proteomic strategies using the protease trypsin (known as bottom-up proteomics) were the first to be developed and optimized and form the dominant approach at present. However, researchers are now beginning to understand the limitations of bottom-up techniques, namely the inability to characterize and quantify intact protein molecules from a complex mixture of digested peptides. To overcome these limitations, several laboratories are taking a whole-protein-based approach, in which intact protein molecules are the analytical targets for characterization and quantification. We discuss these top-down techniques and how they have been applied to clinical research and are likely to be applied in the near future. Given the recent improvements in mass-spectrometry-based proteomics and stronger cooperation between researchers, clinicians and statisticians, both peptide-based (bottom-up) strategies and whole-protein-based (top-down) strategies are set to complement each other and help researchers and clinicians better understand and detect complex disease phenotypes.
authors.affiliation: Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence, 2145 N. Sheridan Dr, Evanston, IL 60208, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Savaryn
authors.affiliation: Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence, 2145 N. Sheridan Dr, Evanston, IL 60208, USA.
authors.forename: Adam D
authors.initials: AD
authors.lastname: Catherman
authors.affiliation: Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence, 2145 N. Sheridan Dr, Evanston, IL 60208, USA.
authors.forename: Paul M
authors.initials: PM
authors.lastname: Thomas
authors.affiliation: The Comprehensive Transplant Center, 676 N. St Clair, Chicago IL 60611, USA.
authors.forename: Michael M
authors.initials: MM
authors.lastname: Abecassis
authors.affiliation: Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence, 2145 N. Sheridan Dr, Evanston, IL 60208, USA ; The Robert H Lurie Comprehensive Cancer Center, 303 E. Superior, Chicago, IL 60611, USA.
authors.forename: Neil L
authors.initials: NL
authors.lastname: Kelleher